Ligand-RNA interaction assay based on size-selective fluorescence core-shell nanocomposite
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RESEARCH PAPER
Ligand-RNA interaction assay based on size-selective fluorescence core-shell nanocomposite Jun Li 1 & Man Wang 1 & Yao-Yao Fan 1 & Hui-Ling Duan 1 & Xu Deng 1 & Zhi-Qi Zhang 1 Received: 16 June 2020 / Revised: 4 August 2020 / Accepted: 6 August 2020 # Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract The application of the dye-labeled fluorescence method in a ligand-RNA interaction assay is a complex and costly process prone to steric hindrance. Fluorescent nanomaterials offer an attractive alternative due to their simple, low-cost synthesis and effective screening properties. Here, CdTe@ZIF-8 core-shell nanocomposites were used as fluorescence signal transducer in the ligandTAR RNA interaction assay. Different experimental strategies were developed based on the size-selective nature of the CdTe@ZIF-8 nanocomposites. When ligands can quench fluorescence, two assays of fluorescence recovery with TAR RNA and Tat peptide competitive displacement are carried out successively, which can not only distinguish ligands binding to TAR RNA but also screen potential Tat protein antagonists. When ligands cannot quench fluorescence, the mitoxantrone-TAR RNA complex is used in the competitive displacement assay. Ligands that displaced mitoxantrone from the mitoxantrone-TAR RNA complex signaled the interaction with TAR RNA. Eight ligands, including known and unknown TAR RNA-binding ligands, were tested via the above strategies. The results showed that this method was effective at distinguishing the known RNA-binding partner and screening the Tat antagonist from the test ligands. This simple and effective strategy is expected to be suitable for actual drug screening. Keywords Ligand-TAR RNA interaction . Core-shell nanocomposites . Size-selective effect . Tat antagonist . Competitive displacement assay
Introduction The diversity of the structure and functions of RNA makes it an irreplaceable target for lead drugs and small-molecule chemical probes [1], and the development of drugs to treat RNA-related diseases is of great significance. Some drugs based on biological molecules, such as antisense oligonucleotides (ASOs) [2] and oligomeric peptides [3, 4], have strong specificity and can act on the lesion site precisely. However, high molecular weight and poor cell penetration require Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00216-020-02869-1) contains supplementary material, which is available to authorized users. * Zhi-Qi Zhang [email protected] 1
Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, 620 West Chang’an Street, Xi’an 710119, Shaanxi, China
complex drug delivery systems to transport them into cells [5, 6]. By contrast, small-molecule drugs can easily penetrate the cell membrane [7–9], and the stability and diversity of such drugs provide us with a deeper understanding of the principles and methods used to treat RNA-related diseases
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